The sudden swift away from classrooms due to the pandemic outbreak, students and faculty members had greatly challenged in the lectures, practical examination of documents presentation of examined signatures and submissions of specimens used in signature and document comparison. This qualitative research used thematic analysis in describing the challenges among the third-year students who were enrolled in Forensic Questioned Documents Examination at the Data Center College of the Philippines. The researcher found out several themes under the category of lectures which includes: Accessibility of recorded discussion and limited lecture time while in the Assessment this includes: themes of multiple online platforms and platform interruptions and lastly, as to Laboratory activity, themes were identified as development and reliability of specimens, quality resolution of uploaded standard specimen and self-study in which it was attributed to the problems encountered by the students in the course of Forensic Questioned Document Examination. Hence, the result of the study implied that creation of a system with specialized features intended for signature/handwriting comparison is highly encouraged.